A plant breeding landscape

Transcription

1 A plant breeding landscape

2 To come Crop improvement in time Breeder s limits and needs Suggestions for science NBTs Durable resistance

3 Towards 2*less - 2* more - 2* better revenues costs Crop improvement in time In research Coming to market Hybrid breeding GM traits Molecular markers GM Transient Genomic selection NovelBreed Techn. (GM) Next 3.0 Design era Computational era Technology era Fertilizer Ancient breeding and seletcion Classic Crop breeding protection Time Classic era Nature given era Agronomic/Food AgChemical AgChemPharma AgChemPharmaIEnergy

4 Introduction HZPC Group Since 1898; origin Netherlands Number of employees: 262 (FTE) Sales of seed potatoes ton Export/license ca. 75 varieties to 82 countries Sales of table potatoes ton Turnover 275 mio; gm <15%; profit ca 5 mio. Shareholders: staff - growers - breeders Sectors

5 Market success is a 4-fold balance AgroPhysio Quality Resistances Value chain satisfaction Achieved by breeding and marketing (60/40; 40/60 ~ 50/50) Breeding: about control of heritable traits or performance and speed of recombination

6 Geographically spread French Fry Factories 23 juli

7 HZPC R&D MOLECULAR BIOLOGY & BIOINFORMATICS QUALITY PRE BREEDING R&D Centre in Netherlands 6 internal + 30 contract breeders annually single hills 7 million mini tubers Selection in climates Towards Genomic breeding PHYTOPATHOLOGY TRIAL SYSTEM Pre & Sector Breeding QUANTITATIVE GENETICS QUALITY & FYSIOLOGY

8 Breeder s limitations genes * 15 effective alleles is 600k of influences + epigenetical Challenge to make the best choice in 600k * 600k opportunities, fixed in series of quadruplex sets of performance. 100k potential crosses at present; <1000 are selected by phenotype, offspring, markers and statistical approaches. Potato breeding is still subjective at start; rely on yield measurement starts when <3% of initial genetic variation ( single hills ) is left 8 yrs to identify the variety, 3 yrs to convince added value to customer and produce seed potato volume

9 Breeder s needs Become more objective with an effective start at crossing and single hill: Baseline is available Phase 1: improved by MAB for resistance Pi R genes, (cyst) nematodes, virus and more; supported by validation protocols for diseases, objective phenotyping, additive genes in a good germplasm background running and achievable, next, Phase 2: grow towards genomic breeding based on performance associated series of SNPs, control allelic contributions, supportive data systems. Phase 3:

10 Research What s needed in/from collaboration with science: Suggestions/challenges: Breeders that can handle the output Affordable FTO; more tools is less per unit Tuberosum reference genomessssss Broad Data handling systems Physiology know how (close the gap towards >100 structural tons/ha) Low-no mistake sequencers or an array for all important alleles, or both Non gm NBT s to solve/fixation simple traits Innovative approaches to unravel complex traits Potato companies understand your work better so Take big steps, Think big, Act collaborative, Focus, Achieve goals in time, Communicate active, Catch spinn-off more Blue sky Know how Applied Deliverable Half Product Product Practical

11 Complexity to come to a logic predictable performance 60-70% 15-25% 15-20% 100% GENOTYPE + ENVIRONMENT + MANAGEMENT => PHENOTYPE Controlled input Variable component modelling / DSS Interactive result DNA sequence, genotyping by sequencing, genomic data Epigenome Methylation RNA: arrays RNAseq micro RNA s Climatic data Consumer preferences Detailed metadata Physiology Control DSS QC s Storage.. Field performance Plant architecture, growth rate, development, etc. Physiological status Proteins Metabolites Other compounds

12 HZPC Challenges (at random) Feed the world, locally (food security, carbon print) Availability sweet water (salinity) High production on poor soils (-2 input, +2 output, better food) Raw product storage at low risk (resistances, physiology) Low-no losses in the value chain (now 40% food waste) Climate extremes within growing season (physiolology) Secure an affordable legal ownership (build a world wide business) Fair profit for future developments (People Planet Profit, Corporate Governance) Consistent product on marketable yield & quality (measure, monitor) Potato is a great carrier to serve all items! Staple crop nr 4 now, Potential to move up to 3!

13 Novel Breeding Technologies

14 Novel breeding technologies 1. Mutation like : SDN1-3, ODM, TALEN, CRISPr, RTDS; techniques can knock out 1 bp up to introduction of genes, protein based or mimic natural repair mechanisms 2. Virus induced gene silencing: (transient) gene silencing mostly used for scientific complementation 3. Cisgenesis: A. tum introduced, only native crossable genes, <20 bp new 4. Grafting: non gm grafted on gm 5. Reverse genetics: redesign parental lines from a hybrid, contains a recombinant step to suppress the meiotic phase 6. RNA dependent DNA methylation; epigenetic change induced by dsrna methylation 7. Agroinfiltration: local expression of foreign genes, parts of plant can be used for cuttings etc. 8...

15 EU Important to know that EU2001/18/EC is process ÁND product based!!! Also the Cartagena protocol is Product and Process based Article 2(2) Definition GMO: Part 1: GMO means an organism, with the exception of human beings, in which the genetic material has been altered in a way that does not occur naturally by mating and/or...= PRODUCT based Part 2: genetic modification occurs at least through the use of techniques listed in Annex 1A part 1 and the techniques listed in Annex 1A part 2 are not considered to result in genetic modification= PROCES based Article 3 is about the application of a gm technique to an organism but will not lead to a GM, listed in Article 1B. Legal landscape: scientific base is is <40%, EU lawyers must be comfortable when taken to court is >60%

16 Durability of resistance Definition: a resistance that holds over many years of agricultural use in various environments, challanged by pathogen recombination and selection in time. CF9 (downey mildew tomato), Mlo (downey mildew wheat), H1 (Potato cyst nematode), Ve1 (Verticillium s tomato) Cf9: appears to be 2-3 genes, not one; mimic by Cisgenesis Mlo: Susceptibility genes knocked out, hard to replace; reverse mimic by HIGS H1: highly effective, still to be cloned and learn why durable Ve1: apparently gene for gene response with Ave1 Achilles heel

17 Potato varieties with Pi R-genes Innovator, Santé, Escort, Toluca, Bionica, Carolus, Sarpo Mira, Biogold, Fresco, Connect, Raja, Athlete, Coquine, Voyager, Janine, etc.. About 10 different R-genes from ca. 5 species are or have been present in listed potato varieties Aim: Durable Disease Resistance Resistance that remains effective over long periods of widespread agricultural use

18 Cisgenic ~ mimic durable Cf9 / wild species approach 2013, Kwang Ryong Jo, Unveiling and deploying durability of late blight resistance in potato, thesis. Year Genotype R-gene content Delay in days & relative

19 Durable resistance: Nature will win, Varieties should hold long.. Strategies to enhance durability of resistance Pyramid/stack multiple genes increase evolutionary hurdle Utilize durable or non-host resistance Match life expectancy of resistance and cultivar Diversify selection pressure on pathogen heterogeneity of resistance genes in space and/or time: diversify resistance sources, host & non-hosts pipeline with different resistance genes, shaping syn- and allopatric evolution, multilines and cultivar mixtures.

20 THE BOOM-AND-BUST CYCLE OF DISEASE CONTROL The Agricultural Consequences of Pathogen Evolution INCREASE IN ACREAGE INTRODUCTION OF RESISTANT VARIETY PATHOGEN CHANGES TO RENDER RESISTANCE INEFFECTIVE DEVELOPMENT OF DECREASE IN ACREAGE RESISTANT VARIETY (Suneson, 1960)

21 Host Induced Gene Silencing Of six genes tested, two (HAM34 & Cellulose Synthase) resulted in inhibition of B. lactucae: Transgenic T 3 lettuce seedlings expressing RNAi HAM34 are resistant to B. lactucae (8 dpi) WT (control) RNAi HAM34 RNAi GUS (control) Diana * (control) Susceptible Resistant Susceptible Resistant Kindly provided by: Richard Michelmoore - Manjula Govindarajulu * Incompatible Interaction

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